ligand-gated channels

[ukemi]

Some ligand-gated channels are not being classified correctly as receptors, see the 'acetylcholine-gated cation-selective channel activity'. Some of these are also being mis-classified as mechanoreceptors. We need to re-examine the logical definitions of all these terms.

[bmeldal]

related tickets:

https://github.com/geneontology/go-ontology/issues/11978 I don't think everything the ticket says has been done is actually visible... The Comment is still there even though David OS said he'd deleted it.

https://github.com/geneontology/go-ontology/issues/9085 Rebecca removed the references to nicotinic and muscarinic but I think we need them systematically as synonyms as that's what these receptors are known as - even though they are external compounds.

I spent a considerable amount of time on these a while ago, notes are here: https://docs.google.com/document/d/1OmYM_1mkln_oSDCygVzSzoHqbXVrrcjthC9wQImG3-I/edit?usp=sharing

Complexes can be found in the CP by searching with "acetylcholine".

[ukemi]

@pgaudet @thomaspd I think it is best to bring you in on this since I'm not sure how you have decided to handle these kinds of functions in the MF overhaul.

[pgaudet]

Hi @ukemi

I though the 'gated' aspect covered the binding; if it's OK with Paul we can add 'receptor activity' as a second parent for all ligand-gated channels. That's consistent with the definition of receptor activity.

Pascale

[ukemi]

Hi @pgaudet ,

I played around with doing that yesterday, it would solve this issue, but is all 'ligand-gated channel activity' a type of receptor activity? I was particularly concerned about the 'intracellular X gated ion channels'. If we think all of the subclasses are receptors, then this is ok. There is also the issue that the bound molecules are defined as being regulated by the binding event. It seems funny that it would be both regulated by acetylcholine binding and has input acetylcholine. Is there something missing?

[pgaudet]

Hi @ukemi

what are the intracellular gated channels ?

There are 'intracellularLY gated channels - ie the ATP is bound on the internal side.

A suggestion for the logical definition: -'regulated by' ~ the gating agent

• 'has input' ~ the transported molecule

Would that work ?

Thanks, Pascale

[ukemi]

That wouldn't work. In the case of acetylcholine receptor activity, it has_input acetylcholine. So if we look at the nicotinic acetylcholine receptors, that would be equivalent to having the transported ion as input. Tranports or maintains localization of is not a subproperty of has_input. It is a sibling and a child of has_participant.

The key question here is are all ligand-gated channels types of receptors.

[ukemi]

Receptor activity is defined as 'Combining with an extracellular or intracellular messenger to initiate a change in cell activity'. So I guess ligand-gated channel activity could be considered a type of receptor activity. It would be nice to better formalize the generic parents.

[ukemi]

@huaiyumi , can you shed any light on this? Would you consider intracellular ligand-gated ion channels like the calcium-release channels or the intracellularly ATP-gated ion channels (PMID:9755289) to be receptors?

[ukemi]

Actually @huaiyumi, as @BarbaraCzub and I looked at this terms more closely, we think there is a lot of potential (pun intended) work to do here. Maybe the three of us could meet at some point and look at them together?